1Misc(3) User Contributed Perl Documentation Misc(3)
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6 PDL::IO::Misc - misc IO routines for PDL
7
9 Some basic I/O functionality: FITS, tables, byte-swapping
10
12 use PDL::IO::Misc;
13
15 bswap2
16 Signature: (x(); )
17 Swaps pairs of bytes in argument x()
19 bswap2 does not process bad values. It will set the bad-value flag of
21 all output piddles if the flag is set for any of the input piddles.
22 bswap4
24 Signature: (x(); )
25 Swaps quads of bytes in argument x()
27 bswap4 does not process bad values. It will set the bad-value flag of
29 all output piddles if the flag is set for any of the input piddles.
30 bswap8
32 Signature: (x(); )
33 Swaps octets of bytes in argument x()
35 bswap8 does not process bad values. It will set the bad-value flag of
37 all output piddles if the flag is set for any of the input piddles.
38 rcols
40 Read specified ASCII cols from a file into piddles and perl arrays
41 (also see "rgrep").
42 Usage:
44 ($x,$y,...) = rcols( *HANDLE|"filename", { EXCLUDE => '/^!/' }, $col1, $col2, ... )
45 $x = rcols( *HANDLE|"filename", { EXCLUDE => '/^!/' }, [] )
46 ($x,$y,...) = rcols( *HANDLE|"filename", $col1, $col2, ..., { EXCLUDE => '/^!/' } )
47 ($x,$y,...) = rcols( *HANDLE|"filename", "/foo/", $col1, $col2, ... )
48 For each column number specified, a 1D output PDL will be generated.
50 Anonymous arrays of column numbers generate 2D output piddles with dim0
51 for the column data and dim1 equal to the number of columns in the
52 anonymous array(s).
53 An empty anonymous array as column specification will produce a single
55 output data piddle with dim(1) equal to the number of columns
56 available.
57 There are two calling conventions - the old version, where a pattern
59 can be specified after the filename/handle, and the new version where
60 options are given as as hash reference. This reference can be given as
61 either the second or last argument.
62 The default behaviour is to ignore lines beginning with a # character
64 and lines that only consist of whitespace. Options exist to only read
65 from lines that match, or do not match, supplied patterns, and to set
66 the types of the created piddles.
67 Can take file name or *HANDLE, and if no explicit column numbers are
69 specified, all are assumed. For the allowed types, see
70 "Datatype_conversions" in PDL::Core.
71 Options (case insensitive):
73 EXCLUDE or IGNORE
75 - ignore lines matching this pattern (default B<'/^#/'>).
76 INCLUDE or KEEP
78 - only use lines which match this pattern (default B<''>).
79 LINES
81 - a string pattern specifying which line numbers to use.
82 Line numbers start at 0 and the syntax is 'a:b:c' to use
83 every c'th matching line between a and b (default B<''>).
84 DEFTYPE
86 - default data type for stored data (if not specified, use the type
87 stored in C<$PDL::IO::Misc::deftype>, which starts off as B<double>).
88 TYPES
90 - reference to an array of data types, one element for each column
91 to be read in. Any missing columns use the DEFTYPE value (default B<[]>).
92 COLSEP
94 - splits on this string/pattern/qr{} between columns of data. Defaults to
95 $PDL::IO::Misc::defcolsep.
96 PERLCOLS
98 - an array of column numbers which are to be read into perl arrays
99 rather than piddles. Any columns not specified in the explicit list
100 of columns to read will be returned after the explicit columns.
101 (default B<undef>).
102 COLIDS
104 - if defined to an array reference, it will be assigned the column
105 ID values obtained by splitting the first line of the file in the
106 identical fashion to the column data.
107 CHUNKSIZE
109 - the number of input data elements to batch together before appending
110 to each output data piddle (Default value is 100). If CHUNKSIZE is
111 greater than the number of lines of data to read, the entire file is
112 slurped in, lines split, and perl lists of column data are generated.
113 At the end, effectively pdl(@column_data) produces any result piddles.
114 VERBOSE
116 - be verbose about IO processing (default C<$PDL::vebose>)
117 For example:
119 $x = PDL->rcols 'file1'; # file1 has only one column of data
121 $x = PDL->rcols 'file2', []; # file2 can have multiple columns, still 1 piddle output
122 # (empty array ref spec means all possible data fields)
123 ($x,$y) = rcols 'table.csv', { COLSEP => ',' }; # read CSV data file
125 ($x,$y) = rcols *STDOUT; # default separator for lines like '32 24'
126 # read in lines containing the string foo, where the first
128 # example also ignores lines that begin with a # character.
129 ($x,$y,$z) = rcols 'file2', 0,4,5, { INCLUDE => '/foo/' };
130 ($x,$y,$z) = rcols 'file2', 0,4,5, { INCLUDE => '/foo/', EXCLUDE => '' };
131 # ignore the first 27 lines of the file, reading in as ushort's
133 ($x,$y) = rcols 'file3', { LINES => '27:-1', DEFTYPE => ushort };
134 ($x,$y) = rcols 'file3', { LINES => '27:', TYPES => [ ushort, ushort ] };
135 # read in the first column as a perl array and the next two as piddles
137 # with the perl column returned after the piddle outputs
138 ($x,$y,$name) = rcols 'file4', 1, 2 , { PERLCOLS => [ 0 ] };
139 printf "Number of names read in = %d\n", 1 + $#$name;
140 # read in the first column as a perl array and the next two as piddles
142 # with PERLCOLS changing the type of the first returned value to perl list ref
143 ($name,$x,$y) = rcols 'file4', 0, 1, 2, { PERLCOLS => [ 0 ] };
144 # read in the first column as a perl array returned first followed by the
146 # the next two data columns in the file as a single Nx2 piddle
147 ($name,$xy) = rcols 'file4', 0, [1, 2], { PERLCOLS => [ 0 ] };
148 NOTES:
151 1. Quotes are required on patterns or use the qr{} quote regexp syntax.
153 2. Columns are separated by whitespace by default, use the COLSEP option
155 separator to specify an alternate split pattern or string or specify an
156 alternate default separator by setting C<$PDL::IO::Misc::defcolsep> .
157 3. Legacy support is present to use C<$PDL::IO::Misc::colsep> to set the
159 column separator but C<$PDL::IO::Misc::colsep> is not defined by default.
160 If you set the variable to a defined value it will get picked up.
161 4. LINES => '-1:0:3' may not work as you expect, since lines are skipped
163 when read in, then the whole array reversed.
164 5. For consistency with wcols and rcols 1D usage, column data is loaded
166 into the rows of the pdls (i.e., dim(0) is the elements read per column
167 in the file and dim(1) is the number of columns of data read.
168 wcols
170 Write ASCII columns into file from 1D or 2D piddles and/or 1D listrefs efficiently.
171 Can take file name or *HANDLE, and if no file/filehandle is given
173 defaults to STDOUT.
174 Options (case insensitive):
176 HEADER - prints this string before the data. If the string
178 is not terminated by a newline, one is added. (default B<''>).
179 COLSEP - prints this string between columns of data. Defaults to
181 $PDL::IO::Misc::defcolsep.
182 FORMAT - A printf-style format string that is cycled through
184 column output for user controlled formatting.
185 Usage: wcols $data1, $data2, $data3,..., *HANDLE|"outfile", [\%options]; # or
187 wcols $format_string, $data1, $data2, $data3,..., *HANDLE|"outfile", [\%options];
188 where the $dataN args are either 1D piddles, 1D perl array refs,
190 or 2D piddles (as might be returned from rcols() with the [] column
191 syntax and/or using the PERLCOLS option). dim(0) of all piddles
192 written must be the same size. The printf-style $format_string,
193 if given, overrides any FORMAT key settings in the option hash.
194 e.g.,
196 $x = random(4); $y = ones(4);
198 wcols $x, $y+2, 'foo.dat';
199 wcols $x, $y+2, *STDERR;
200 wcols $x, $y+2, '|wc';
201 $a = sequence(3); $b = zeros(3); $c = random(3);
203 wcols $a,$b,$c; # Orthogonal version of 'print $a,$b,$c' :-)
204 wcols "%10.3f", $a,$b; # Formatted
206 wcols "%10.3f %10.5g", $a,$b; # Individual column formatting
207 $a = sequence(3); $b = zeros(3); $units = [ 'm/sec', 'kg', 'MPH' ];
209 wcols $a,$b, { HEADER => "# a b" };
210 wcols $a,$b, { Header => "# a b", Colsep => ', ' }; # case insensitive option names!
211 wcols " %4.1f %4.1f %s",$a,$b,$units, { header => "# Day Time Units" };
212 $a52 = sequence(5,2); $b = ones(5); $c = [ 1, 2, 4 ];
214 wcols $a52; # now can write out 2D pdls (2 columns data in output)
215 wcols $b, $a52, $c # ...and mix and match with 1D listrefs as well
216 NOTES:
218 1. Columns are separated by whitespace by default, use
220 C<$PDL::IO::Misc::defcolsep> to modify the default value or
221 the COLSEP option
222 2. Support for the C<$PDL::IO::Misc::colsep> global value
224 of PDL-2.4.6 and earlier is maintained but the initial value
225 of the global is undef until you set it. The value will be
226 then be picked up and used as if defcolsep were specified.
227 3. Dim 0 corresponds to the column data dimension for both
229 rcols and wcols. This makes wcols the reverse operation
230 of rcols.
231 swcols
233 generate string list from "sprintf" format specifier and a list of
234 piddles
235 "swcols" takes an (optional) format specifier of the printf sort and a
237 list of 1D piddles as input. It returns a perl array (or array
238 reference if called in scalar context) where each element of the array
239 is the string generated by printing the corresponding element of the
240 piddle(s) using the format specified. If no format is specified it uses
241 the default print format.
242 Usage: @str = swcols format, pdl1,pdl2,pdl3,...;
244 or $str = swcols format, pdl1,pdl2,pdl3,...;
245 rgrep
247 Read columns into piddles using full regexp pattern matching.
248 Options:
251 UNDEFINED: This option determines what will be done for undefined
253 values. For instance when reading a comma-separated file of the type
254 C<1,2,,4> where the C<,,> indicates a missing value.
255 The default value is to assign C<$PDL::undefval> to undefined values,
257 but if C<UNDEFINED> is set this is used instead. This would normally
258 be set to a number, but if it is set to C<Bad> and PDL is compiled
259 with Badvalue support (see L<PDL::Bad/>) then undefined values are set to
260 the appropriate badvalue and the column is marked as bad.
261 DEFTYPE: Sets the default type of the columns - see the documentation for
263 L</rcols()>
264 TYPES: A reference to a Perl array with types for each column - see
266 the documentation for L</rcols()>
267 BUFFERSIZE: The number of lines to extend the piddle by. It might speed
269 up the reading a little bit by setting this to the number of lines in the
270 file, but in general L</rasc()> is a better choice
271 Usage
273 ($x,$y,...) = rgrep(sub, *HANDLE|"filename")
275 e.g.
277 ($a,$b) = rgrep {/Foo (.*) Bar (.*) Mumble/} $file;
279 i.e. the vectors $a and $b get the progressive values of $1, $2 etc.
281 rdsa
283 Read a FIGARO/NDF format file.
284 Requires non-PDL DSA module. Contact Frossie (frossie@jach.hawaii.edu)
286 Usage:
288 ([$xaxis],$data) = rdsa($file)
290 $a = rdsa 'file.sdf'
292 Not yet tested with PDL-1.9X versions
294 isbigendian
296 Determine endianness of machine - returns 0 or 1 accordingly
297 rasc
299 Simple function to slurp in ASCII numbers quite quickly,
300 although error handling is marginal (to nonexistent).
301 $pdl->rasc("filename"|FILEHANDLE [,$noElements]);
303 Where:
305 filename is the name of the ASCII file to read or open file handle
306 $noElements is the optional number of elements in the file to read.
307 (If not present, all of the file will be read to fill up $pdl).
308 $pdl can be of type float or double (for more precision).
309 # (test.num is an ascii file with 20 numbers. One number per line.)
311 $in = PDL->null;
312 $num = 20;
313 $in->rasc('test.num',20);
314 $imm = zeroes(float,20,2);
315 $imm->rasc('test.num');
316 rcube
318 Read list of files directly into a large data cube (for efficiency)
319 $cube = rcube \&reader_function, @files;
321 $cube = rcube \&rfits, glob("*.fits");
323 This IO function allows direct reading of files into a large data cube,
325 Obviously one could use cat() but this is more memory efficient.
326 The reading function (e.g. rfits, readfraw) (passed as a reference) and
328 files are the arguments.
329 The cube is created as the same X,Y dims and datatype as the first
331 image specified. The Z dim is simply the number of images.
332
334 Copyright (C) Karl Glazebrook 1997, Craig DeForest 2001, 2003, and
335 Chris Marshall 2010. All rights reserved. There is no warranty. You are
336 allowed to redistribute this software / documentation under certain
337 conditions. For details, see the file COPYING in the PDL distribution.
338 If this file is separated from the PDL distribution, the copyright
339 notice should be included in the file.
340perl v5.28.1 2019-02-14 Misc(3)